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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGGTTCATAAACAGAACTAAGCCGCAACTAAGCAAAGATCAGCAACAAAACCTTACCAGATGGGCAGTGAgttatacttccatctctcttggcctaacagaaacagaaccatgtcatagcctaaatgtcggttgatgccgttcttttggtatttcag

Basic information

species Zea mays
transcript GRMZM2G004352_T01
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G004352_T01 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os04g54640.1 (Oryza sativa), 5'ss of exon 9
AGGTTCATAAACAGAACTAAGCCGCAACTAAGCAAAGATCAGCAACAAAACCTTACCAGATGGGCAGTGAgttatacttccatct-ctcttggcctaacagaaacagaaccatgtcatagcctaaatgtcggttgatgccgttcttttggtat-ttcag---------
|| ||||||||| | |||||||||| | ||| ||| |||||||||||||||||||| |||||||||||||||| |   |  ||    | |||  |||  ||| ||| || | ||  | |     | |   |     |    || |||| | || ||| |         
AGATTCATAAACCGGACTAAGCCGCCATTAACCAAGGATCAGCAACAAAACCTTACAAGATGGGCAgtgagttgtctgtttattaatttttgaactagaagacaca-aatcgtgctacatatcgattaatgcagagtttttttttttttgaatcttctggttttgtag

upper sequence: GRMZM2G004352_T01 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os04g54640.2 (Oryza sativa), 5'ss of exon 9
AGGTTCATAAACAGAACTAAGCCGCAACTAAGCAAAGATCAGCAACAAAACCTTACCAGATGGGCAGTGAgttatacttccatct-ctcttggcctaacagaaacagaaccatgtcatagcctaaatgtcggttgatgccgttcttttggtatttcag
|| ||||||||| | |||||||||| | ||| ||| |||||||||||||||||||| |||||||||||||||| |   |  ||    | |||  |||  ||| ||| || | ||       ||| || ||| || |||| |                 
AGATTCATAAACCGGACTAAGCCGCCATTAACCAAGGATCAGCAACAAAACCTTACAAGATGGGCAgtgagttgtctgtttattaatttttgaactagaagacaca-aatcgtg-------ctacatatcgattaatgcag-----------------

upper sequence: GRMZM2G004352_T01 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA08G14970.1 (Glycine max), 5'ss of exon 9
AGGTTCATAAACAGAACTAAGCCGCAACTAAGCAAAGATCAGCAACAAAACCTTACCAGATGGGCAGTGAgttat--acttccatctctctt---ggcctaacagaaacagaaccatgtcatagcctaaatgtcggttgatgccgttcttttggtatttcag
|| || || |||||||| ||||| |  || |||||||||||||||||||| || || |||||||||||  ||| |  | | | |||| | ||    |  | | |   ||  ||        |||||    |||  | | | |  | || |      || |||
AGATTTATTAACAGAACCAAGCCACCCCTCAGCAAAGATCAGCAACAAAATCTCACAAGATGGGCAgtatgttttcaaatactatctatgtttacagtttgataagtaccaaaaataaatgtagcccttttgt--gcttaagaagctcatg----gttgcag

upper sequence: GRMZM2G004352_T01 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA05G31720.1 (Glycine max), 5'ss of exon 9
AGGTTCATAAACAGAACTAAGCCGCAACTAAGCAAAGATCAGCAACAAAACCTTACCAGATGGGCAGTGAgttat--acttccatctctcttggcctaacagaaacagaaccatgtcatagcctaaatgtcggttgatgccgttcttttggtatttcag--------
|| || || |||||||| ||||| | ||| |||||||||||||||||||| || || |||||||| ||  ||| |  | | |||| | | ||    | | | | ||  ||         |||    |  |   |  ||     |  ||    |  |||         
AGATTTATTAACAGAACCAAGCCACCACTCAGCAAAGATCAGCAACAAAATCTCACAAGATGGGCCgtatgtttttaaataccatatatgttta--tgataaatacctaaaataaatgcagctctcaaatttatgcatttttgtgcttaaaaagctcatgtttgcag

upper sequence: GRMZM2G004352_T01 (Zea mays), 5'ss of exon 9
lower sequence: Vv07s0031g01560.t01 (Vitis vinifera), 5'ss of exon 9
AGGTTCATAAACAGAACTAAGCCGCAACTAAGCAAAGATCAGCAACAAAACCTTACCAGATGGGCAGTGAgttatacttccatctctcttggcctaacagaaa-cagaacca--tgtcatagcctaaatgtcggttgatgccgttcttttggtatttcag-----------
|| || |||||| | |  ||||| || || |||||||||||||||||||| |||||||||||||| |||||||  |          |  |||||  ||      |||  |||  ||   ||    |    | | |   |      | | |  |     |            
AGATTTATAAACCGTAGCAAGCCACAGCTCAGCAAAGATCAGCAACAAAATCTTACCAGATGGGCTgtgagttccatccatcataataatggccagactttcttcagtgccacttgcagtatttgatgaattgatgagttttaaccatataatgggcaaaaaatgatgcag

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|18167877|gb|BM337717.1|BM337717
EST:     GCCGCAACTAAGCAAAGATCAGCAACAAAACCTTACCAGATGGGC----A                         GTCCTGTTTGCTGCATCACTTCTGAAGAACAACAAAGCAGCCCATGAGGCG
genomic: GCCGCAACTAAGCAAAGATCAGCAACAAAACCTTACCAGATGGGCAGTGAgttatacttc ... ggtatttcagGTCCTGTTTGCTGCATCACTTCTGAAGAACAACAAAGCAGCCCATGAGGCG
EST: gi|149100297|gb|EE186362.2|EE186362
EST:     GCCGCAACTAAGCAAAGATCAGCAACAAAACCTTACCAGATGGGC----A                         GTCCTGTTTGCTGCATCACTTCTGAAGAACAACAAAGCAGCCCATGAGGCG
genomic: GCCGCAACTAAGCAAAGATCAGCAACAAAACCTTACCAGATGGGCAGTGAgttatacttc ... ggtatttcagGTCCTGTTTGCTGCATCACTTCTGAAGAACAACAAAGCAGCCCATGAGGCG
EST: gi|76010526|gb|DT937696.1|DT937696
EST:     GCCGCAACTAAGCAAAGATCAGCAACAAAATCTTACCAGATGGGCAGT--                         --CCTGTTTGCTGCATCACTTCTGAAGAACA-CAAAGCAGCCCATGAGGCG
genomic: GCCGCAACTAAGCAAAGATCAGCAACAAAACCTTACCAGATGGGCAGTGAgttatacttc ... ggtatttcagGTCCTGTTTGCTGCATCACTTCTGAAGAACAACAAAGCAGCCCATGAGGCG
EST: gi|91872112|gb|EB402069.1|EB402069
EST:     GCCGCAACTAAGCAAAGATCAGCAACAAAACCTTACCAGATGGGC----A                         GTCCTGTTTGTTGCATCACTTTTGAAGAACAACAAAGCAGCCCATGAGGCG
genomic: GCCGCAACTAAGCAAAGATCAGCAACAAAACCTTACCAGATGGGCAGTGAgttatacttc ... ggtatttcagGTCCTGTTTGCTGCATCACTTCTGAAGAACAACAAAGCAGCCCATGAGGCG
EST: gi|149100298|gb|EE186363.2|EE186363
EST:     GCCGCAACTAAGCAAAGATCAGCAACAAAACCTTACCAGATGGGCAGT--                         --CCTGTTTGCTGCATCACTTCTGAAGA-CAACAAAGCAGCCCA
genomic: GCCGCAACTAAGCAAAGATCAGCAACAAAACCTTACCAGATGGGCAGTGAgttatacttc ... ggtatttcagGTCCTGTTTGCTGCATCACTTCTGAAGAACAACAAAGCAGCCCA
EST: gi|71317337|gb|DR795362.1|DR795362
EST:     GCCGCAACTAAGCAAAGATCAGCAACAAAACCTTACCAGATGGGC----A                         GTCCTGTTTGCTGCATCACTTCTGAAGAACAACAAAGCAGCCCATGAGGCG
genomic: GCCGCAACTAAGCAAAGATCAGCAACAAAACCTTACCAGATGGGCAGTGAgttatacttc ... ggtatttcagGTCCTGTTTGCTGCATCACTTCTGAAGAACAACAAAGCAGCCCATGAGGCG
EST: gi|148930743|gb|EC873038.2|EC873038
EST:     GCCGCAACTAAGCAAAGATCAGCAACAAAACCTTACCAGATGGGCAGTGA                         GTCCTGTTTGCTGCATCACTTCT
genomic: GCCGCAACTAAGCAAAGATCAGCAACAAAACCTTACCAGATGGGCAGTGAgttatacttc ... ggtatttcagGTCCTGTTTGCTGCATCACTTCT
EST: gi|148954648|gb|EC900095.2|EC900095
EST:     AAGCAAAGATCAGCAACAAAACCTTACCAGATGGGC----A                         GTCCTGTTTGCTGCATCACTTCTGAAGAACAACAAAGCAGCCCATGAGGCG
genomic: AAGCAAAGATCAGCAACAAAACCTTACCAGATGGGCAGTGAgttatacttc ... ggtatttcagGTCCTGTTTGCTGCATCACTTCTGAAGAACAACAAAGCAGCCCATGAGGCG
EST: gi|71317339|gb|DR795363.1|DR795363
EST:     CCGCA-CTAAGCAAAGATCAGCAACAAAAACTTTAC-AGATGGGCAGT--                         --CCTGTTTGCTGCATCACTTTCTGA
genomic: C-GCAACTAAGCAAAGATCAGCAACAAAACCTT-ACCAGATGGGCAGTGAgttatacttc ... ggtatttcagGTCCTGTTTGCTGCATCACTT-CTGA

Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGGTTCATAAACAGAACTAAGCCGCAACTAAGCAAAGATCAGCAACAAAACCTTACCAGATGGGCAGTGAgttatacttccatctctcttggcctaacagaaacagaaccatgtcatagcctaaatgtcggttgatgccgttcttttggtatttcag

- - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - -  AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG